BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926919.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 30,409,822 number of mapped reads = 27,008,414 (88.81%) number of supplementary alignments = 500,668 (1.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,570,186 number of mapped paired reads (second in pair) = 13,438,228 number of mapped paired reads (both in pair) = 26,548,068 number of mapped paired reads (singletons) = 460,346 number of mapped bases = 2,478,218,610 bp number of sequenced bases = 2,476,390,777 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,131,425 duplication rate = 6.41% >>>>>>> Insert size mean insert size = 189,739.2211 std insert size = 4,293,401.4402 median insert size = 184 >>>>>>> Mapping quality mean mapping quality = 52.9154 >>>>>>> ACTG content number of A's = 696,688,890 bp (28.13%) number of C's = 496,524,930 bp (20.05%) number of T's = 703,261,200 bp (28.4%) number of G's = 579,698,911 bp (23.41%) number of N's = 216,846 bp (0.01%) GC percentage = 43.46% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 25,402,159 number of insertions = 392,938 mapped reads with insertion percentage = 1.43% number of deletions = 1,272,390 mapped reads with deletion percentage = 4.59% homopolymer indels = 52.24% >>>>>>> Coverage mean coverageData = 0.8005X std coverageData = 2.5822X There is a 32.61% of reference with a coverageData >= 1X There is a 17.73% of reference with a coverageData >= 2X There is a 10.1% of reference with a coverageData >= 3X There is a 6.2% of reference with a coverageData >= 4X There is a 3.95% of reference with a coverageData >= 5X There is a 2.6% of reference with a coverageData >= 6X There is a 1.75% of reference with a coverageData >= 7X There is a 1.21% of reference with a coverageData >= 8X There is a 0.84% of reference with a coverageData >= 9X There is a 0.6% of reference with a coverageData >= 10X There is a 0.43% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.23% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 211068374 0.8468118280034296 2.535732825747627 chr2 243199373 218007342 0.8964140791596531 3.592010209752548 chr3 198022430 171101277 0.864049981610669 1.7770533816702334 chr4 191154276 144283990 0.7548038841673623 1.8076054845922762 chr5 180915260 147574816 0.8157123727429074 1.7035254306807506 chr6 171115067 141284281 0.8256682680082169 1.7189353714139388 chr7 159138663 125803491 0.7905275099615484 1.8300646783467873 chr8 146364022 127546234 0.8714316008615833 1.9476439822985152 chr9 141213431 102123912 0.7231883771735566 2.6623064638254754 chr10 135534747 124177362 0.9162031489976515 6.779347431569751 chr11 135006516 121041634 0.8965614222649816 2.0467843434310775 chr12 133851895 115206153 0.8606987073287233 1.8409769195719652 chr13 115169878 73000793 0.6338531764355955 1.4960039558827163 chr14 107349540 75650159 0.7047087393201685 1.6470305873961695 chr15 102531392 78339136 0.7640502530190949 1.7728829674558977 chr16 90354753 80855388 0.8948659070541646 3.468956852435106 chr17 81195210 68598699 0.8448614025384009 1.9459018263318621 chr18 78077248 65083408 0.8335771260790339 2.647623967552421 chr19 59128983 43253162 0.7315052585971249 1.929834249672529 chr20 63025520 60860656 0.9656509934388483 1.988658793342483 chr21 48129895 17666564 0.36706009851049953 1.8221398404172975 chr22 51304566 33575210 0.6544292763338062 1.6786021599379135 chrMT 16571 4992 0.3012491702371613 0.6923011779689561 chrX 155270560 128337328 0.8265399957338982 1.7758525971686465 chrY 59373566 3774249 0.06356783421093488 1.5753288221691462